- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Distortion of transmission spectra due to particle size
by Scott Calvin 24 Nov '10

24 Nov '10

Some follow-up. This, for example, is from an excellent workshop presentation by Rob Scarrow: > Errors from large particles are independent of thickness > The relative (%) variation in thickness depends on the ratio > (particle diameter / avg. thickness), so it is tempting to increase > the avg. thickness (i.e. increase μx) as an alternative to reducing > the particle diameter. > However, simulations of MnO2 spectra for average Δμ0x = 1, 2 or 3 > show that the errors in derived pre-edge peak heights and EXAFS > amplitude factors are significant when diameter > 0.2 / Δμ0, but > that they are not affected by the average sample thickness. (Δμ0 > refers to the edge jump) > The equation at right is given by Heald (quoting earlier work by > Stern and Lu). D is particle diameter, μ1 is for just below the > edge, and Δμ =μ(above edge) - μ1. I've seen similar claims elsewhere, although Scarrow's is particularly clear and unambiguous. The equation Scarrow gives is indeed the one from Lu and Stern, and the simulations are based on that equation. That Lu-Stern equation is derived for a monolayer of spheres, and then experimentally tested with multiple layers of tape. I'm still trying to work through the math to see how it works for multiple layers. I'm not convinced that the N divides out as is claimed in the article. As Matt says, it wasn't their main point. There is no question that if the particle size is large compared to an absorption length there will be nonuniformity and thus distortions. But compare a monolayer of particles with a diameter equal to 0.4 absorption lengths with four strips of tape of that kind stacked. Do we really think the distortion due to nonuniformity will be as bad in the latter case as in the first? In practice, I think many transmission samples fall in roughly that regime, so the question isn't just academic. I'll keep trying to work through the math and let you know what I find. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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maximum number of paths in Artemis
by Bruce Ravel 23 Nov '10

23 Nov '10

Yuan, It seems unwise to post a new question at the end of a long and active thread. Presumably you are looking for an answer -- hiding your question at the end of another thread does not seem like a good way to get that answer. That said, the answer to the question of how to get more than 512 paths depends on your operating system. For Mac: See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-October/009673.html For Windows: You will need the ifeffit dll compiled with more paths. Matt, does such a thing exist for the current version of the dll? If you are using linux, let us know. It is not hard to recompile everything to do what you need. I can write up a short howto. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Transmission EXAFS sample
by Jatinkumar Rana 23 Nov '10

23 Nov '10

On 22.11.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Transmission EXAFS sample (Scott Calvin) > 2. Re: Transmission EXAFS sample (Scott Calvin) > 3. maximum number of paths in Artemis (Yuan Ping) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 22 Nov 2010 07:13:42 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<5B5040D9-F501-4BA0-8F24-38630B43B943(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > To my mind, when considering sample preparation the important thing is > not so much the "right" thickness, as knowing the effects to guard > against as the thickness deviates toward the thin or thick side. > > As transmission samples become thicker, the problem of "unwanted" > photons becomes more severe. Those photons may be harmonics, photons > scattered into the It detector, or photons from the tails of the > resolution curve of the monochromator. > > As transmission samples become thinner, uniformity becomes more of an > issue. If you play with the equations, you'll see that if your sample > is a mixture of regions that have a thickness of 1.0 absorption > lengths and regions that have a thickness of 2.0 absorption lengths, > the spectrum is less distorted than if it is a mixture of 0.5 and 1.0 > absorption lengths. > > So if a sample is on the thick side, it is particularly important to > guard against harmonics in the beam and scattered photons. If it is on > the thin side, it is particularly important to guard against > nonuniformity. > > To put it another way, problems are synergistic. With a well- > conditioned beam, a uniform sample, and linear detectors, the > thickness almost doesn't matter (within reason)--at a modern beamline, > a total absorption of even 0.05 or 4.0 will work. > > But as each of those conditions deviates from the ideal, distortions > become much more severe. > > There's an old joke about someone on a diet going in to a fast food > joint and asking for a double bacon cheeseburger, a large fries...and > a diet Coke. In XAFS measurements, that attitude actually kind of > works, because of the synergies I just discussed. > > Personally, I trust my ability to condition the beam and minimize > scattering more than I trust my ability to make a uniform sample, so I > lean a little toward the thicker side. > > --Scott Calvin > Faculty at Sarah Lawrence College > Currently on sabbatical at Stanford Synchrotron Radiation Laboratory > > > > On Nov 22, 2010, at 5:13 AM, Welter, Edmund wrote: > > >> Dear Jatin, >> >> the optimum mued of 2.x is not just derived by simple photon counting >> statistics. As Matt pointed out, for transmission measurements at a >> synchrotron beamline in conventional scanning mode this is seldom a >> matter. Nevertheless, one should avoid to measure subtle changes of >> absorption at the extreme ends, that is, transmission near 0 % or >> 100 %. >> In optical photometry this is described by the more or less famous >> "Ringbom plots" which describe the dependency of the accuracy of >> quantitative analysis by absorption measurements (usually but not >> necessarily in the UV/Vis) from the total absorption of the sample. >> >> This time the number is only near to 42, the optimum transmission is >> 36.8 % (mue = 1). So, to achieve the highest accuracy in the >> determination of small Delta c (c = concentration) you should try to >> measure samples with transmissions near to this value (actually the >> minimum is broad and transmissions between 0.2 and 0.7 are ok). In our >> case, we are not interested in the concentration of the absorber, >> but we >> are also interested in (very) small changes of the transmission resp. >> absorption in our samples. Or, using Bouger, Lambert Beer's law, in >> our >> case mue (-ln(I1/I0) is a function of the absorption coefficient >> (mue0). >> The concentration of the absorber and the thickness (d) of the sample >> are constant. >> >> -ln(I1/I0) = mue0 * c * d >> >> But then: If the optimum is a mue between 0.35 and 1.6 why are we all >> measuring successfully (ok, more or less ;-) using samples having a >> mue >> between 2 and 3? ...and 0.35 seems desperately small to me! Maybe >> sample >> homogeneity is an issue? >> >> Cheers, >> Edmund Welter >> >> >> > > > ------------------------------ > > Message: 2 > Date: Mon, 22 Nov 2010 07:16:06 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<3730BF4F-966F-46E3-9784-B5FB8EF5310D(a)gmail.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > > On Nov 22, 2010, at 7:09 AM, Jatinkumar Rana wrote: > >>> >> Hi Scott, >> >> Sorry for mixing up the things. >> >> For the case, when i have very limited amount of sample that i can not >> cover 1sq.cm area, you, Matt and others have given very very clear >> explanation about possible solutions and the probable effects on data >> quality. I am really very thankful to all of you for sharing your >> experience and expertise. >> >> My last post was with reference to the case when i have enough powders >> (i.e., reference oxide compounds). It is just to be ensured that i am >> doing things 100% exactly in a same way it has to be done. >> >> With best regards, >> Jatin >> >> -- >> Jatinkumar Rana >> >> > Yes, Jatin, the procedure you described is fine. There is no "right" > way to make samples, although there are many wrong ways. > > --Scott Calvin > Faculty at Sarah Lawrence College > Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

On Nov 21, 2010, at 2:45 AM, Jatinkumar Rana wrote: >> >> > Hi Scott, > > Yes I have assumed the sample cross section area to be 1 sq. cm. and > then calculated the amount of sample required for that. > > What i planned is following : > > I would calculate the amount of sample required for 1sq.cm area, take > that amount of sample and make it very fine paste using mortar and > pestle, and then apply it uniformly on a piece of kapton tape. Then > fold > the tape over and over again in such a way that final bunch of tapes > will yield to 1 sq.cm. area containing the required amount of sample. > > Will it be the right approach ?? OR I can take randomly few milligrams > of powder (i.e. not strictly as per calculation) and make a several > uniform layers of tape ?? > > With best regards, > Jatin > > -- Hi Jatin, I'm not sure I understand. If you have enough sample for the 1 square centimeter target, then there shouldn't be a problem, right? I was assuming from your initial question that you weren't going to have enough sample to do that. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Distortion of transmission spectra due to particle size
by Scott Calvin 22 Nov '10

22 Nov '10

Hi all, I'm tracking down a piece of EXAFS lore which I think is incorrect. I've seen it said that you cannot compensate for the distortion introduced by large particle sizes by making the sample thicker. Certainly thick samples have their own set of issues (e.g. "thickness effects" from harmonics), but I've seen the claim that the mathematics of the distortions introduced by nonuniformity means that there is a particle-size distortion that is independent of thickness. This claim is sometimes accompanied by an equation giving chi_eff/chi_real as a function of particle size diameter D and various absorption coefficients. I've eventually traced this equation back to a paper by Lu and Stern from 1983, have walked through the derivation, and believe there is a flaw in the logic that has led to the erroneous--and widely quoted-- conclusion that thickness cannot compensate for particle size. The paper, for those who want to follow along, is K. Lu and E. A. Stern, "Size effect of powdered sample on EXAFS amplitude," Nucl. Instrm. and Meth. 212, 475-478 (1983). They calculate the intensity transmitted by a spherical particle, and from there calculate the attenuation in the normalized EXAFS signal for a beam passing through that particle. They then, however, extend this to multiple layers of particles by the following argument: "Finally, the attenuation in N layers is given by (I/I0)^N, where I is the transmitted intensity through one layer. Xeff for N layers is then the same as for a single layer since N will cancel in the final result." This is not the case, is it? It seems to me that their analysis assumes that the spheres in subsequent layers line up with the spheres in previous ones, so that thick spots are always over thick and thin spots over thin. It's little wonder, then, that making the sample thicker does not improve the uniformity according to that analysis. I've done a calculation for the effects of uniformity in a somewhat different way, and found that it is indeed true that multiple layers on particles show less distortion due to nonuniformity that a single layer of particles of the same size, just as one would intuitively imagine, and in contrast to Lu and Stern. Do you agree that the extrapolation to multiple layers in the original Lu and Stern paper is not correct, or have I misled myself somehow? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory P.S. None of this should be taken as an endorsement of overly thick samples! Harmonics and the like are a concern regardless of the uniformity issue.

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

To my mind, when considering sample preparation the important thing is not so much the "right" thickness, as knowing the effects to guard against as the thickness deviates toward the thin or thick side. As transmission samples become thicker, the problem of "unwanted" photons becomes more severe. Those photons may be harmonics, photons scattered into the It detector, or photons from the tails of the resolution curve of the monochromator. As transmission samples become thinner, uniformity becomes more of an issue. If you play with the equations, you'll see that if your sample is a mixture of regions that have a thickness of 1.0 absorption lengths and regions that have a thickness of 2.0 absorption lengths, the spectrum is less distorted than if it is a mixture of 0.5 and 1.0 absorption lengths. So if a sample is on the thick side, it is particularly important to guard against harmonics in the beam and scattered photons. If it is on the thin side, it is particularly important to guard against nonuniformity. To put it another way, problems are synergistic. With a well- conditioned beam, a uniform sample, and linear detectors, the thickness almost doesn't matter (within reason)--at a modern beamline, a total absorption of even 0.05 or 4.0 will work. But as each of those conditions deviates from the ideal, distortions become much more severe. There's an old joke about someone on a diet going in to a fast food joint and asking for a double bacon cheeseburger, a large fries...and a diet Coke. In XAFS measurements, that attitude actually kind of works, because of the synergies I just discussed. Personally, I trust my ability to condition the beam and minimize scattering more than I trust my ability to make a uniform sample, so I lean a little toward the thicker side. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 22, 2010, at 5:13 AM, Welter, Edmund wrote: > Dear Jatin, > > the optimum mued of 2.x is not just derived by simple photon counting > statistics. As Matt pointed out, for transmission measurements at a > synchrotron beamline in conventional scanning mode this is seldom a > matter. Nevertheless, one should avoid to measure subtle changes of > absorption at the extreme ends, that is, transmission near 0 % or > 100 %. > In optical photometry this is described by the more or less famous > "Ringbom plots" which describe the dependency of the accuracy of > quantitative analysis by absorption measurements (usually but not > necessarily in the UV/Vis) from the total absorption of the sample. > > This time the number is only near to 42, the optimum transmission is > 36.8 % (mue = 1). So, to achieve the highest accuracy in the > determination of small Delta c (c = concentration) you should try to > measure samples with transmissions near to this value (actually the > minimum is broad and transmissions between 0.2 and 0.7 are ok). In our > case, we are not interested in the concentration of the absorber, > but we > are also interested in (very) small changes of the transmission resp. > absorption in our samples. Or, using Bouger, Lambert Beer's law, in > our > case mue (-ln(I1/I0) is a function of the absorption coefficient > (mue0). > The concentration of the absorber and the thickness (d) of the sample > are constant. > > -ln(I1/I0) = mue0 * c * d > > But then: If the optimum is a mue between 0.35 and 1.6 why are we all > measuring successfully (ok, more or less ;-) using samples having a > mue > between 2 and 3? ...and 0.35 seems desperately small to me! Maybe > sample > homogeneity is an issue? > > Cheers, > Edmund Welter > >

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

On Nov 22, 2010, at 7:09 AM, Jatinkumar Rana wrote: >> > Hi Scott, > > Sorry for mixing up the things. > > For the case, when i have very limited amount of sample that i can not > cover 1sq.cm area, you, Matt and others have given very very clear > explanation about possible solutions and the probable effects on data > quality. I am really very thankful to all of you for sharing your > experience and expertise. > > My last post was with reference to the case when i have enough powders > (i.e., reference oxide compounds). It is just to be ensured that i am > doing things 100% exactly in a same way it has to be done. > > With best regards, > Jatin > > -- > Jatinkumar Rana > Yes, Jatin, the procedure you described is fine. There is no "right" way to make samples, although there are many wrong ways. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Re: [Ifeffit] Transmission EXAFS sample
by Jatinkumar Rana 22 Nov '10

22 Nov '10

On 21.11.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Transmission EXAFS sample (Jatinkumar Rana) > 2. Re: Transmission EXAFS sample (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Nov 2010 11:44:25 +0100 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To:ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<4CE8F809.3040208(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 20.11.2010 19:00,ifeffit-request@millenia.cars.aps.anl.gov wrote: > >> Send Ifeffit mailing list submissions to >> ifeffit(a)millenia.cars.aps.anl.gov >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> or, via email, send a message with subject or body 'help' to >> ifeffit-request(a)millenia.cars.aps.anl.gov >> >> You can reach the person managing the list at >> ifeffit-owner(a)millenia.cars.aps.anl.gov >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Ifeffit digest..." >> >> >> Today's Topics: >> >> 1. Re: Transmission EXAFS sample (Scott Calvin) >> 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 19 Nov 2010 10:30:37 -0800 >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Hi Jatin, >> >> Matt covered most of what I would say, but I'll add a few comments of >> my own. >> >> I'm not sure how you arrived at the conclusion that you have only a >> few percent of what you need--you must be assuming a sample area >> somehow. I have frequently made transmission measurements on samples >> where I only had a few milligrams available. Generally, I did it by >> spreading it on a layer of tape as well as I could and then folding >> the tape over and over again--sometimes to make as many as 16 layers. >> (Of course, that many layers is not advisable if you're below 6 keV or >> so, as the absorption of the tape itself would kill the signal). Even >> if there are lots of pinholes because you can't cover the tape >> effectively, 16 layers from folding will make them cancel out fairly >> well. I can then narrow the beam a bit to match the size of my sample. >> Flux isn't really the issue here, so I don't even need a focussed >> beamline--I can just narrow the slits. >> >> Two other tips: >> >> 1) Realize that even with a tiny amount of sample that much of it >> won't end up on the tape. The process of brushing on tape is designed >> to separate the small grains from the big ones, with only the small >> ones ending up on tape. Allow that to happen! >> >> 2) You can sometimes get a second piece of tape to have some sample on >> it by putting it sticky side down on your mortar and peeling it back. >> A thin layer of dust from the sample will stick to the tape, and give >> you a little more absorption and a bit more of a uniform distribution. >> If you stack that with the primary piece of tape and then fold a few >> times, you may end up in pretty good shape, as long as you're not >> operating at a low enough energy so that all the layers of tape are a >> problem.. >> >> This procedure doesn't give me the best data I've ever seen, but it's >> often not bad. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: >> >> >> >>> Dear Jatin, >>> >>> The idea that the optimum absorption length (mu*t) for transmission >>> experiments is 2.3 assumes that the errors in the measurement are due >>> to counting statistics of the x-rays. For any synchrotron experiment, >>> the number of x-rays in the transmission chamber is high enough that >>> the noise from counting statistics is rarely significant. This means >>> that using a value of 2.3 is really not that important. >>> >>> The more important issues are >>> a) having a uniform sample. >>> b) not having (mu*t) so high that higher-order harmonics dominate >>> the transmission measurement. >>> >>> For transmission measurements, it's difficult to overstate the >>> importance of a uniform sample. For an ideal thickness, I would say >>> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >>> step of 0.1 to 1.0, and a total absorption less than 3.0. >>> >>> If you only have enough material for an edge step as low as 0.02 (as >>> you imply), then measuring in fluorescence or electron emission is >>> probably a better choice. Such a sample won't be severely affected by >>> "self-absorption" (or "over absorption" to use the term this mailing >>> list prefers) in the fluorescence measurement. I would recommend >>> simultaneously measuring transmission and florescence for such a >>> sample. >>> >>> My concern about a very thin sample is uniformity. Specifically, is >>> the grain size really well below mu/0.02 so that a collection of >>> particles can give a uniform thickness? Since you didn't give any >>> details of the system, it's hard to guess. >>> >>> Is it feasible to pack that material into a smaller area so that the >>> thickness is increased and use a smaller x-ray beam? >>> >>> >>> >>>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>>> calculated based on above fact) required, and still i can perform >>>> transmission EXAFS ? How would this affect my data ? (I guess, it >>>> will be >>>> heavily dominated by noise) >>>> >>>> >>> I would guess that a sample with mu*t of 0.02 would be dominated by >>> pinholes. >>> >>> >>> >>>> -- What if, i have required amount of sample but since material's >>>> density is >>>> so high that it yields only small volume of powder (for a given >>>> weight), >>>> that it can not be covered up on multiple layers of Kapton tape to >>>> ensure >>>> pinhole-free sample ? >>>> >>>> >>> If you cannot get the grain size small enough to have many overlapping >>> grains in the sample, the sample won't be uniform enough for good >>> transmission data. The techniques of using multiple layers of mixing >>> with a low-Z binder don't solve this problem. These do help to make a >>> uniform collection of overlapping grains, but don't make the grains >>> smaller. >>> >>> I would recommend trying to increase the thickness at the expense of >>> cross-sectional area, and/or measuring in both transmission and >>> fluorescence. >>> >>> Hope that helps, >>> >>> --Matt >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 19 Nov 2010 23:21:43 -0500 >> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> >> Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; >> DelSp="Yes" >> >> That's probably how they discovered graphene, by trying to make exafs >> sample. >> Anatoly >> >> Sent from my mobile phone, please forgive typos. >> >> -----Original message----- >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> >> >>

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Re: [Ifeffit] Ifeffit Digest, Vol 93, Issue 16
by Jatinkumar Rana 22 Nov '10

22 Nov '10

On 21.11.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Transmission EXAFS sample (Jatinkumar Rana) > 2. Re: Transmission EXAFS sample (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Nov 2010 11:44:25 +0100 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<4CE8F809.3040208(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 20.11.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > >> Send Ifeffit mailing list submissions to >> ifeffit(a)millenia.cars.aps.anl.gov >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> or, via email, send a message with subject or body 'help' to >> ifeffit-request(a)millenia.cars.aps.anl.gov >> >> You can reach the person managing the list at >> ifeffit-owner(a)millenia.cars.aps.anl.gov >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Ifeffit digest..." >> >> >> Today's Topics: >> >> 1. Re: Transmission EXAFS sample (Scott Calvin) >> 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 19 Nov 2010 10:30:37 -0800 >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Hi Jatin, >> >> Matt covered most of what I would say, but I'll add a few comments of >> my own. >> >> I'm not sure how you arrived at the conclusion that you have only a >> few percent of what you need--you must be assuming a sample area >> somehow. I have frequently made transmission measurements on samples >> where I only had a few milligrams available. Generally, I did it by >> spreading it on a layer of tape as well as I could and then folding >> the tape over and over again--sometimes to make as many as 16 layers. >> (Of course, that many layers is not advisable if you're below 6 keV or >> so, as the absorption of the tape itself would kill the signal). Even >> if there are lots of pinholes because you can't cover the tape >> effectively, 16 layers from folding will make them cancel out fairly >> well. I can then narrow the beam a bit to match the size of my sample. >> Flux isn't really the issue here, so I don't even need a focussed >> beamline--I can just narrow the slits. >> >> Two other tips: >> >> 1) Realize that even with a tiny amount of sample that much of it >> won't end up on the tape. The process of brushing on tape is designed >> to separate the small grains from the big ones, with only the small >> ones ending up on tape. Allow that to happen! >> >> 2) You can sometimes get a second piece of tape to have some sample on >> it by putting it sticky side down on your mortar and peeling it back. >> A thin layer of dust from the sample will stick to the tape, and give >> you a little more absorption and a bit more of a uniform distribution. >> If you stack that with the primary piece of tape and then fold a few >> times, you may end up in pretty good shape, as long as you're not >> operating at a low enough energy so that all the layers of tape are a >> problem.. >> >> This procedure doesn't give me the best data I've ever seen, but it's >> often not bad. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: >> >> >> >>> Dear Jatin, >>> >>> The idea that the optimum absorption length (mu*t) for transmission >>> experiments is 2.3 assumes that the errors in the measurement are due >>> to counting statistics of the x-rays. For any synchrotron experiment, >>> the number of x-rays in the transmission chamber is high enough that >>> the noise from counting statistics is rarely significant. This means >>> that using a value of 2.3 is really not that important. >>> >>> The more important issues are >>> a) having a uniform sample. >>> b) not having (mu*t) so high that higher-order harmonics dominate >>> the transmission measurement. >>> >>> For transmission measurements, it's difficult to overstate the >>> importance of a uniform sample. For an ideal thickness, I would say >>> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >>> step of 0.1 to 1.0, and a total absorption less than 3.0. >>> >>> If you only have enough material for an edge step as low as 0.02 (as >>> you imply), then measuring in fluorescence or electron emission is >>> probably a better choice. Such a sample won't be severely affected by >>> "self-absorption" (or "over absorption" to use the term this mailing >>> list prefers) in the fluorescence measurement. I would recommend >>> simultaneously measuring transmission and florescence for such a >>> sample. >>> >>> My concern about a very thin sample is uniformity. Specifically, is >>> the grain size really well below mu/0.02 so that a collection of >>> particles can give a uniform thickness? Since you didn't give any >>> details of the system, it's hard to guess. >>> >>> Is it feasible to pack that material into a smaller area so that the >>> thickness is increased and use a smaller x-ray beam? >>> >>> >>> >>>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>>> calculated based on above fact) required, and still i can perform >>>> transmission EXAFS ? How would this affect my data ? (I guess, it >>>> will be >>>> heavily dominated by noise) >>>> >>>> >>> I would guess that a sample with mu*t of 0.02 would be dominated by >>> pinholes. >>> >>> >>> >>>> -- What if, i have required amount of sample but since material's >>>> density is >>>> so high that it yields only small volume of powder (for a given >>>> weight), >>>> that it can not be covered up on multiple layers of Kapton tape to >>>> ensure >>>> pinhole-free sample ? >>>> >>>> >>> If you cannot get the grain size small enough to have many overlapping >>> grains in the sample, the sample won't be uniform enough for good >>> transmission data. The techniques of using multiple layers of mixing >>> with a low-Z binder don't solve this problem. These do help to make a >>> uniform collection of overlapping grains, but don't make the grains >>> smaller. >>> >>> I would recommend trying to increase the thickness at the expense of >>> cross-sectional area, and/or measuring in both transmission and >>> fluorescence. >>> >>> Hope that helps, >>> >>> --Matt >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 19 Nov 2010 23:21:43 -0500 >> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> >> Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; >> DelSp="Yes" >> >> That's probably how they discovered graphene, by trying to make exafs >> sample. >> Anatoly >> >> Sent from my mobile phone, please forgive typos. >> >> -----Original message----- >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> >> >>

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Re: [Ifeffit] Transmission EXAFS sample
by Jatinkumar Rana 21 Nov '10

21 Nov '10

On 20.11.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Transmission EXAFS sample (Scott Calvin) > 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 19 Nov 2010 10:30:37 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Jatin, > > Matt covered most of what I would say, but I'll add a few comments of > my own. > > I'm not sure how you arrived at the conclusion that you have only a > few percent of what you need--you must be assuming a sample area > somehow. I have frequently made transmission measurements on samples > where I only had a few milligrams available. Generally, I did it by > spreading it on a layer of tape as well as I could and then folding > the tape over and over again--sometimes to make as many as 16 layers. > (Of course, that many layers is not advisable if you're below 6 keV or > so, as the absorption of the tape itself would kill the signal). Even > if there are lots of pinholes because you can't cover the tape > effectively, 16 layers from folding will make them cancel out fairly > well. I can then narrow the beam a bit to match the size of my sample. > Flux isn't really the issue here, so I don't even need a focussed > beamline--I can just narrow the slits. > > Two other tips: > > 1) Realize that even with a tiny amount of sample that much of it > won't end up on the tape. The process of brushing on tape is designed > to separate the small grains from the big ones, with only the small > ones ending up on tape. Allow that to happen! > > 2) You can sometimes get a second piece of tape to have some sample on > it by putting it sticky side down on your mortar and peeling it back. > A thin layer of dust from the sample will stick to the tape, and give > you a little more absorption and a bit more of a uniform distribution. > If you stack that with the primary piece of tape and then fold a few > times, you may end up in pretty good shape, as long as you're not > operating at a low enough energy so that all the layers of tape are a > problem.. > > This procedure doesn't give me the best data I've ever seen, but it's > often not bad. > > --Scott Calvin > Sarah Lawrence College > > On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: > > >> Dear Jatin, >> >> The idea that the optimum absorption length (mu*t) for transmission >> experiments is 2.3 assumes that the errors in the measurement are due >> to counting statistics of the x-rays. For any synchrotron experiment, >> the number of x-rays in the transmission chamber is high enough that >> the noise from counting statistics is rarely significant. This means >> that using a value of 2.3 is really not that important. >> >> The more important issues are >> a) having a uniform sample. >> b) not having (mu*t) so high that higher-order harmonics dominate >> the transmission measurement. >> >> For transmission measurements, it's difficult to overstate the >> importance of a uniform sample. For an ideal thickness, I would say >> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >> step of 0.1 to 1.0, and a total absorption less than 3.0. >> >> If you only have enough material for an edge step as low as 0.02 (as >> you imply), then measuring in fluorescence or electron emission is >> probably a better choice. Such a sample won't be severely affected by >> "self-absorption" (or "over absorption" to use the term this mailing >> list prefers) in the fluorescence measurement. I would recommend >> simultaneously measuring transmission and florescence for such a >> sample. >> >> My concern about a very thin sample is uniformity. Specifically, is >> the grain size really well below mu/0.02 so that a collection of >> particles can give a uniform thickness? Since you didn't give any >> details of the system, it's hard to guess. >> >> Is it feasible to pack that material into a smaller area so that the >> thickness is increased and use a smaller x-ray beam? >> >> >>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>> calculated based on above fact) required, and still i can perform >>> transmission EXAFS ? How would this affect my data ? (I guess, it >>> will be >>> heavily dominated by noise) >>> >> I would guess that a sample with mu*t of 0.02 would be dominated by >> pinholes. >> >> >>> -- What if, i have required amount of sample but since material's >>> density is >>> so high that it yields only small volume of powder (for a given >>> weight), >>> that it can not be covered up on multiple layers of Kapton tape to >>> ensure >>> pinhole-free sample ? >>> >> If you cannot get the grain size small enough to have many overlapping >> grains in the sample, the sample won't be uniform enough for good >> transmission data. The techniques of using multiple layers of mixing >> with a low-Z binder don't solve this problem. These do help to make a >> uniform collection of overlapping grains, but don't make the grains >> smaller. >> >> I would recommend trying to increase the thickness at the expense of >> cross-sectional area, and/or measuring in both transmission and >> fluorescence. >> >> Hope that helps, >> >> --Matt >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 2 > Date: Fri, 19 Nov 2010 23:21:43 -0500 > From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> > Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; > DelSp="Yes" > > That's probably how they discovered graphene, by trying to make exafs > sample. > Anatoly > > Sent from my mobile phone, please forgive typos. > > -----Original message----- > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 > Subject: Re: [Ifeffit] Transmission EXAFS sample > > >

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 20 Nov '10

20 Nov '10

Hi Jatin, Matt covered most of what I would say, but I'll add a few comments of my own. I'm not sure how you arrived at the conclusion that you have only a few percent of what you need--you must be assuming a sample area somehow. I have frequently made transmission measurements on samples where I only had a few milligrams available. Generally, I did it by spreading it on a layer of tape as well as I could and then folding the tape over and over again--sometimes to make as many as 16 layers. (Of course, that many layers is not advisable if you're below 6 keV or so, as the absorption of the tape itself would kill the signal). Even if there are lots of pinholes because you can't cover the tape effectively, 16 layers from folding will make them cancel out fairly well. I can then narrow the beam a bit to match the size of my sample. Flux isn't really the issue here, so I don't even need a focussed beamline--I can just narrow the slits. Two other tips: 1) Realize that even with a tiny amount of sample that much of it won't end up on the tape. The process of brushing on tape is designed to separate the small grains from the big ones, with only the small ones ending up on tape. Allow that to happen! 2) You can sometimes get a second piece of tape to have some sample on it by putting it sticky side down on your mortar and peeling it back. A thin layer of dust from the sample will stick to the tape, and give you a little more absorption and a bit more of a uniform distribution. If you stack that with the primary piece of tape and then fold a few times, you may end up in pretty good shape, as long as you're not operating at a low enough energy so that all the layers of tape are a problem.. This procedure doesn't give me the best data I've ever seen, but it's often not bad. --Scott Calvin Sarah Lawrence College On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: > Dear Jatin, > > The idea that the optimum absorption length (mu*t) for transmission > experiments is 2.3 assumes that the errors in the measurement are due > to counting statistics of the x-rays. For any synchrotron experiment, > the number of x-rays in the transmission chamber is high enough that > the noise from counting statistics is rarely significant. This means > that using a value of 2.3 is really not that important. > > The more important issues are > a) having a uniform sample. > b) not having (mu*t) so high that higher-order harmonics dominate > the transmission measurement. > > For transmission measurements, it's difficult to overstate the > importance of a uniform sample. For an ideal thickness, I would say > that the better rules of thumb than mu*t = 2.3 are to aim for an edge > step of 0.1 to 1.0, and a total absorption less than 3.0. > > If you only have enough material for an edge step as low as 0.02 (as > you imply), then measuring in fluorescence or electron emission is > probably a better choice. Such a sample won't be severely affected by > "self-absorption" (or "over absorption" to use the term this mailing > list prefers) in the fluorescence measurement. I would recommend > simultaneously measuring transmission and florescence for such a > sample. > > My concern about a very thin sample is uniformity. Specifically, is > the grain size really well below mu/0.02 so that a collection of > particles can give a uniform thickness? Since you didn't give any > details of the system, it's hard to guess. > > Is it feasible to pack that material into a smaller area so that the > thickness is increased and use a smaller x-ray beam? > >> -- Can my sample be only few percentage of the "actual amount" (i.e. >> calculated based on above fact) required, and still i can perform >> transmission EXAFS ? How would this affect my data ? (I guess, it >> will be >> heavily dominated by noise) > > I would guess that a sample with mu*t of 0.02 would be dominated by > pinholes. > >> -- What if, i have required amount of sample but since material's >> density is >> so high that it yields only small volume of powder (for a given >> weight), >> that it can not be covered up on multiple layers of Kapton tape to >> ensure >> pinhole-free sample ? > > If you cannot get the grain size small enough to have many overlapping > grains in the sample, the sample won't be uniform enough for good > transmission data. The techniques of using multiple layers of mixing > with a low-Z binder don't solve this problem. These do help to make a > uniform collection of overlapping grains, but don't make the grains > smaller. > > I would recommend trying to increase the thickness at the expense of > cross-sectional area, and/or measuring in both transmission and > fluorescence. > > Hope that helps, > > --Matt > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

2 1

Transmission EXAFS sample
by Jatinkumar Rana 19 Nov '10

19 Nov '10

Dear all, I have very basic question about the sample preparation for EXAFS. It is well understood and proven by several researchers that the optimum amount of sample (per unit area) required for EXAFS is determined by the fact that the total absorbtion of the entire sample above the absorption edge (of interest) should be between 2 to 2.5, more precisely, it should be 2.3. The reason which forces me to put this question to a mailing list is that, i treat my sample through a process which yields only few percentage of the total amount of sample required for EXAFS. I would prefer to measure EXAFS in transmission mode with samples prepared on several layers of Kapton tape which are bound together to ensure pinhole free sample. My questions are : -- Can my sample be only few percentage of the "actual amount" (i.e. calculated based on above fact) required, and still i can perform transmission EXAFS ? How would this affect my data ? (I guess, it will be heavily dominated by noise) -- What if, i have required amount of sample but since material's density is so high that it yields only small volume of powder (for a given weight), that it can not be covered up on multiple layers of Kapton tape to ensure pinhole-free sample ? I look forward to any comments or suggestions as this would help me improvise the quality of my data. With best regards, Jatin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

3 2

Re: [Ifeffit] Origin of terminology "self-absorption"
by Scott Calvin 17 Nov '10

17 Nov '10

I tried a few searches, but rapidly get lost in other uses of the term. My guess is we borrowed it from some other spectroscopy, much the way we borrowed "Debye-Waller factor" from XRD, and then proceeded to change its meaning. But it would be nice to be able to track that down. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 16, 2010, at 10:54 AM, Matthew Marcus wrote: > It's definitely a misnomer. I use "overabsorption" and encourage > others to do so. I suppose to track it down would require going > back over the seminal papers on the subject. > mam > > On 11/16/2010 10:19 AM, Scott Calvin wrote: >> Hi all, >> >> As some of you know, I'm currently working on a textbook on XAFS >> analysis. Because of that, I'm going to occasionally pose some >> questions for the list that may seem a bit random. I hope none of >> you mind me using the list in this way; the questions may seem to >> come out of left field, but I think they will still be of interest >> to many. >> >> With that said, here's my question for today: >> >> What is the origin of the use of "self-absorption" to describe the >> suppression of fine-structure observed in thick, concentrated >> samples measured in fluorescence? I understand the physics of the >> effect itself, my question is the curious wording. Compared to a >> thin concentrated sample, the effect might better be described as >> "saturation," while compared to a thick dilute sample, it's >> actually related to a lack of absorption by other elements. >> >> --Scott Calvin >> Faculty at Sarah Lawrence College >> Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

4 3

UO2 thin films on STO
by mohamed sobhy 16 Nov '10

16 Nov '10

Dear All I would like to grow UO2 thin films on STO (SrTiO3) substrate but I found that Sr K-edge 16105 and U L3-edge is 17166. Do you think there will be any interference? Best, Mohamed

4 3

Origin of terminology "self-absorption"
by Scott Calvin 16 Nov '10

16 Nov '10

Hi all, As some of you know, I'm currently working on a textbook on XAFS analysis. Because of that, I'm going to occasionally pose some questions for the list that may seem a bit random. I hope none of you mind me using the list in this way; the questions may seem to come out of left field, but I think they will still be of interest to many. With that said, here's my question for today: What is the origin of the use of "self-absorption" to describe the suppression of fine-structure observed in thick, concentrated samples measured in fluorescence? I understand the physics of the effect itself, my question is the curious wording. Compared to a thin concentrated sample, the effect might better be described as "saturation," while compared to a thick dilute sample, it's actually related to a lack of absorption by other elements. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

3 2

help
by Aaron Yevick 12 Nov '10

12 Nov '10

Hi all, I downloaded Artemis twice, from both cars.uchicago and sourceforge. Both times I downloaded the latest, 1.2.11.exe. When it installed, I opened Artemis and was prompted to install several updates. I clicked Install Updates, and both times it says: downloading fetching update 10 (iff_010.zip).... downloaded iff_010.zip OK. expanding file iff_010.zip and goes no further in an hour. I quit. When it runs, along the bottom it says the version is 0.8.012 (c) 2002-2008, which I was told is not the latest version (is that true?) My operating system is Windows 7 Professional. Can anybody offer suggestions as to why this happens? Does it matter if I don't have these updates? Aaron

5 4

Re: [Ifeffit] something is wrong with Ruthenium-Oxygen bond amplitudes
by Scott Calvin 06 Nov '10

06 Nov '10

Hi Maria, What was the physical form of the samples (powder, thin film, etc.) and how were they measured (transmission, fluorescence, ...)? Sometimes this kind of thing can stem from sample/beamline/data effects. --Scott Calvin Sarah Lawrence College On Nov 5, 2010, at 5:50 PM, María Elena Montero Cabrera wrote: > Hello friends, > > Hopping someone could help us. We are having some problems in > fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with > path functions obtained using FEFF 8.4, where we got amplitude > values of less than 0.50 for Ru-O first shells. We think this value > probably is wrong, although there are some publications where some > oxygen deficiency is studied and recorded as true. The ATOMS input > data was found to be ok due to the Rietveld analysis results told us > these are good. The reason we think we may be wrong with something > during the fitting appeared because we tried to fit our reference > sample of RuO2 (measured under same conditions as the experiment of > Ru-Cu at SSRL) and we came to the same results, even worst, of > amplitude lower than 0.40. We are attaching the Artemis files so you > can take a look on it and give us some light to continue with our > analysis. > Thanking in advance, take care

3 3

something is wrong with Ruthenium-Oxygen bond amplitudes
by María Elena Montero Cabrera 06 Nov '10

06 Nov '10

Hello friends, Hopping someone could help us. We are having some problems in fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with path functions obtained using FEFF 8.4, where we got amplitude values of less than 0.50 for Ru-O first shells. We think this value probably is wrong, although there are some publications where some oxygen deficiency is studied and recorded as true. The ATOMS input data was found to be ok due to the Rietveld analysis results told us these are good. The reason we think we may be wrong with something during the fitting appeared because we tried to fit our reference sample of RuO2 (measured under same conditions as the experiment of Ru-Cu at SSRL) and we came to the same results, even worst, of amplitude lower than 0.40. We are attaching the Artemis files so you can take a look on it and give us some light to continue with our analysis. Thanking in advance, take care -- María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

1 0

Re: [Ifeffit] feff question
by Joshua Kas 04 Nov '10

04 Nov '10

Hi George, The obsolete warning is probably not a big deal, however, the compilation should be tested since compiling with gfortran has not been well tested for feff7. If you can get an old version of g77, you won't have issues. Otherwise, I would use the following command when running gfortran. gfortran -finit-local-zero -o feff702 feff702.f This may not work with your version of gfortran (-finit-local-zero is not in the manual) but if it does, the compiled feff will be less likely to have runtime errors. Cheers, Josh Kas I installed gfortran-4.2.3.dmg file on top of the gfortran-42-5577.pkg and > can now see "gfortran" in '/usr/local/bin'. I am also able to compile > simple > fortran code, but when I attempt to run Feff7 I get the following message: > > bash-3.2$ /usr/local/bin/gfortran -o feff702 feff702.f > feff702.f:12161.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > feff702.f:12226.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > bash-3.2$ > > Any idea as to what the problem is now? > > Thank you, > George > > > > On Wed, Nov 3, 2010 at 3:45 PM, Matt Newville <newville(a)cars.uchicago.edu > >wrote: > > > Hi George, > > > > On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky > > <GeorgeSterbinsky(a)u.northwestern.edu> wrote: > > > I've also noticed that there is not a file or directory called gfortran > > in > > > '/usr/local/bin'. This is what made me think I may also need to install > > the > > > gfortran-4.2.3.dmg file. If I do not see a file or directory called > > gfortran > > > in '/usr/local/bin' does this indicate that gfortran is not installed? > Is > > it > > > possible that gfortran-42-5577.pkg placed it somewhere else? > > > > Yes, those are all possible. You need to install gfortran, find out > > where it is, and then run it to compile and link feff702 into an > > executable. It sounds like you might want to get a local unix-savvy > > person who can help you.... > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

2 1

feff question
by George Sterbinsky 03 Nov '10

03 Nov '10

Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX version 10.5.8) starting from the feff702.f file. Thank you, George

3 10

Scripting - Python
by Andrew Korinda 01 Nov '10

01 Nov '10

I'm looking to introduce some scripting routines to some of my EXAFS fitting work. Looking around I ran across the Python module and downloaded that. The shell works fine, as does enter commands directly into Ifeffit, however I'm not getting the read and write commands to work from within Python scripts. Example: iff.ifeffit("read_data(C:\Program Files\Ifeffit\examples\Ifeffit\data\cu10k.chi,group=c)") returns -1. >From this experience I have some questions: ~First does anyone have some debugging tips for cross talk problems? The Fortran return values are fine, but would returning the echo_buffer or a log file be more helpful? ~Secondly, Does anyone have any example Python scripts for Ifeffit that they would like to share? I'm new to Python and haven't done programming for a while and I'd like to get a better idea of what's all possible, and how. I was looking at Matt Newville's message back in 2008 about defining a library for Athena in Python and his 2001 paper but couldn't find much else. ~Finally, would I be better off coding in Perl and using Demeter? Thanks everyone, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University

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"Hard tests failed in fovrg"
by srihari velaga 29 Oct '10

29 Oct '10

Hi all, I am trying to fit Cd kedge EXAFS data of CdO and CdO-CaO solid solution. Like many others I ended with “Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small“error. Professor John, mentioned this may be due to insufficient grid size in calculating the phase shifts and he advised to post the "feff.inp", to have a look at it. But I have 38 feff.inp files in total (corresponding to CdO, solid solutions of CdO-CaO at various compositions and for dopents as well). I feel it will be hard to look into this may files, for any one. I will be thankful if anyone help me, in how to overcome this problem. Here with I am attaching the "feff.inp" of CdO. Please tell me how to modify feff.inp file such that I can do myself for the rest of feff files Thanks in advance. Srihari. V VELAGA.SRIHARI, DAE RESEARCH FELLOW, X-RAY AND CRYSTAL GROWTH SECTION, MATERIAL SCIENCE DIVISION, INDIRA GANDHI CENTRE FOR ATOMIC RESEARCH, KALPAKKAM,TAMILNADU-603102, INDIA.

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

Yes; it's a case of trying to distinguish between a few boulders and lots of pebbles; the total volume isn't the issue. What I'm looking at is something like surface/volume ratio, but with "surface" being path-dependent and gradual. For a nearest-neighbor path, only the top monolayer of atoms are on the surface. For a 5 angstrom path, the transition region from "surface" to "core" extends 5 angstroms in. But that more sophisticated definition of "surface" doesn't change the fact that the dominant dependence is 1/R, so that should address the issue. --Scott Calvin Sarah Lawrence College On Oct 25, 2010, at 4:43 AM, Matt Newville wrote: > Hi Scott, > > That's a pretty amazing use case. > > But I'm not sure I understand the issue exactly right. I would have > thought the volume (r**3) was the important physical parameter, and > that a 1000nm particle would dominate the spectra over 3nm particles. > Or is it that you are trying to distinguish between 1 very large > crystal or 100s of smaller crystals? Perhaps the effect you're > really trying to account for is the surface/volume ratio? If so, I > think using Matthew Marcus's suggestion of using 1/r (with a safety > margin) makes the most sense. > > --Matt >

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Re: [Ifeffit] LCF analysis
by Scott Calvin 25 Oct '10

25 Oct '10

On Oct 25, 2010, at 8:25 AM, Wayne W Lukens Jr wrote: > A more useful way to look at this is that the probabilities that A, > B and C are present are 99.99999999%, 93%, and 77%, respectively. An excellent post, Wayne, but I don't think that last statement is quite right. If the F-test gives a probability of 0.23 for material C, I believe it's saying that there is a 23% that, given the noise level in the data, the fit would indicate that C was present when it was not. That is not the same thing as saying there is a 77% chance of C being present. To see this, imagine very, very noisy data. Including C in the fit might very well improve the fit in the sense of an R-factor--maybe, in fact, there's a 45% chance of a modest improvement with a given set of very noisy data, even if there's no C present. That does not mean that a result like that should lead to the conclusion that C is more likely than not present (55%). --Scott Calvin Sarah Lawrence College

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LCF analysis
by Luxton.Todd＠epamail.epa.gov 25 Oct '10

25 Oct '10

I have a general question for the group. How do you conduct your LCF fitting routine? Do most people allow Eo to vary for the standards, or force the weights of all of the combinations to 1? How do people judge a significant improvement to the resulting goodness of fit parameters? I am aware of most of the pitfalls associated with LCF analysis of XAFS data (over fitting data with too many standards, not having information to support the use of a standard in the fit, ect.). What I am really interested in is how people fit and judge the quality of a fit after collecting all of the necessary background information? Or, what is the process/routine people go through during LCF analysis? I have looked at older threads on the IFEFFIT web page, but I was unable to find a description of the general process people follow. Additionally, if anyone is aware of a reference discussing the potential problems and/or solutions to fitting data using LCF that would be great. All the Best Todd

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